/*
 * Copyright 2010-2012 Susanta Tewari. <freecode4susant@users.sourceforge.net>
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package genomemap.tagging;

import genomemap.data.Clone;
import genomemap.data.Gene;

/**
 *
 * @author stewari1
 */
public class SeqTaggingStrategy extends TaggingStrategy {

    /**
     * Constructs ...
     */
    public SeqTaggingStrategy() {}

    @Override
    public void tag() {

        for (Clone clone : clones) {

            if (clone.hasSeqInfo() &&!clone.isTagged()) {

                for (Gene gene : genes) {

                    if (!gene.isTagged() && clone.isOverLapping(gene)) {

                        gene.addTaggedClone(clone);
                        clone.addTaggedGene(gene);

                        break;
                    }
                }
            }
        }
    }
}
